When rebel forces took over Syria, they pledged to unite the country’s disparate armed groups into a unified national army.

The biggest challenge for them by far has been in northeastern Syria, an autonomous region run by the country’s Kurdish minority where suspicion of the new leadership runs deep.

In past years, the rebels and the Kurds fought each other. But with the rebels now governing Syria, they are working to form an alliance and merge the powerful Kurdish-led military into the new national force.

Interviews with dozens of people in the northeast in late March revealed that Kurdish distrust of the new government is rooted partly in the fact that the former rebels now in charge were once affiliated with Al Qaeda. Some Kurds are also wary because the new government is backed by Turkey, which has tried for years to undercut Kurdish power in Syria.

“How can we trust this new government in Damascus?” asked Amina Mahmoud, 31, a Kurdish resident of the northeastern town of Kobani.

Her skepticism is shared by other members of Syria’s diverse range of ethnic and religious minorities, who worry that the new government will not protect, include or represent them.

The Kurdish-led Syrian Democratic Forces, or S.D.F., agreed on March 10 to integrate its military and other institutions, including its prized oil and gas fields, under the central government’s control by year’s end. It was a major breakthrough for the new Syrian president, Ahmed al-Shara, in his efforts to unify a country still wrestling with violent turmoil.

In the last month, the Kurds began to reduce their military presence in the major northeastern city of Aleppo and the two sides exchanged prisoners even as the rhetoric on both sides has become more confrontational, underscoring the long history of tensions.

Initially, the merger deal had been applauded in the northeast — an area with a mixed population of Arabs and Kurds that is administered by a Kurdish-led regional government. The Kurds, who make up about 10 percent of Syria’s population, particularly welcomed a provision in the accord stipulating that they would have the same rights as other Syrians.

But doubts quickly surfaced.

Members of the regional government described the agreement as merely a first step. Important details have yet to be worked out, such as whether the S.D.F. will join the national military as a bloc or have a continuing role in securing the northeast.

“Al-Shara and the new government want to control all of Syria,” said Badran Kurdi, a Kurdish political figure who took part in the merger negotiations with Mr. al-Shara. “And of course they are dreaming about controlling all of our areas. But it’s very difficult.”

Ali Ahmed, 55, a Kurd from the northeastern city of Hasakah who teaches chemistry, called Mr. al-Shara “a terrorist.” He spoke as his family enjoyed a picnic in the countryside to celebrate the spring festival of Nowruz, the Persian new year.

“We know him,” he said.

He was referring to the period from 2013 to 2016, when Mr. al-Shara led Al Qaeda’s Syrian affiliate, the Nusra Front. During those years, the Nusra Front fought a number of battles against the S.D.F. over control of several northeastern towns. Mr. al-Shara now speaks of reconstruction and inclusion.

As Mr. Ahmed looked across a haze of greening fields toward the Turkish border, barely 10 miles away, he said that Mr. al-Shara’s close ties with Turkey only added to his doubts.

But not all Kurds see the deal as a negative.

One senior member of the Kurdish political leadership, Salih Muslim, said that despite the distance between the two sides, he sees this as a historic opportunity for Kurds to gain recognition from the government.

Inextricably woven into every conversation, however, were questions about whether the deal will stop Turkey’s attacks on Syrian Kurds.

Turkey links Kurdish fighters in Syria’s northeast to the Kurdish militants inside Turkey who have been fighting the government for more than 40 years. For the past several years, Turkey has been launching air attacks on Syrian Kurdish-forces across the border and has also supported Syrian proxy forces against the Kurds.

The Turkish military initially kept up some drone attacks and airstrikes even after Mr. al-Shara and the S.D.F. leader, Mazloum Abdi, signed the merger accord. But it has now suspended the attacks.

One of the deadliest Turkish strikes since the accord hit a farming hamlet outside the Kurdish-majority town of Kobani in March. It killed a family of farm laborers — a couple and their eight children, the youngest 7 months old, according to Firas Qassim Lo, the farmer they were working for, and the Syrian Democratic Forces.

Turkey denied killing the family and said in a statement that its operations “exclusively target terrorist organizations.” Turkey routinely refers to the S.D.F. as “terrorists.”

There was no indication that anyone connected to the Kurdish-led force was in the family’s home when it was struck.

A funeral for the family drew more than a thousand Kurds who lined a road leading to a small cemetery in Kobani. Each of the coffins, a photo of the deceased taped to the outside, was hoisted onto the shoulders of local men and carried to the burial ground.

Ms. Mahmoud, the Kurdish resident of Kobani, lives in an apartment overlooking the cemetery and watched with tears in her eyes.

“Why does Erdogan do this to us? What have we done?” she said, referring to Turkey’s president, Recep Tayyip Erdogan.

Shortly after the Kobani strike, Turkey largely suspended its attacks on the S.D.F., as did its Syrian proxy forces.

Some Christians, who practice their faith openly in the northeast, sounded fearful of any agreement that would allow Mr. al-Shara’s military forces to deploy there.

Their fears were heightened last month by violence directed primarily at another Syrian minority, the Alawites, in two northwestern provinces along the Mediterranean coast. The violence began when loyalists of the ousted dictator Bashar al-Assad attacked the new government’s forces.

The soldiers responded, but so did thousands of others fighters, including foreign fighters and armed groups nominally linked to the new government. About 1,600 people were killed, most of them civilians from the Alawite minority, which the Assad family belongs to.

Alis Marderos, 50, an Armenian Christian in the northeastern town of Qamishli, said that the Kurds needed to remain in charge of security. “If the Kurds did not exist here, we would have been beheaded,” she said after attending Sunday Mass at the Armenian Orthodox church.

For years, the United States has given military, financial and political support to the S.D.F. after deeming it the ground force most capable of defeating the Islamic State, the terrorist group that took over a large swath of Syrian territory during the civil war. U.S. troops have maintained a small presence in northeastern Syria for years but began this month to draw them down.

After years of fighting, the S.D.F. managed to wrest back all the territory captured by the Islamic State.

Some Arab residents of the northeast said they were pleased with the deal because it would bring the S.D.F. under the control of the central government, which they see as a needed check on Kurdish power. Arabs, who are the majority ethnic group in Syria, were divided, however, on the role they want the Kurdish-led forces to play in the future.

Sheikh Hassan al Muslat al-Milhim, an Arab Syrian from Hasakah, said he resented the power of the S.D.F. in a region that has a large Arab population. The American support for the force made things worse, in his view, by augmenting its power.

“We the Arabs, up until this moment, do not like having the Americans here,” said Mr. al-Milhim. He said he had appreciated Mr. al-Shara’s approach when he led the Nusra Front and was active in the northeast.

“They respected us, they helped us,” Mr. al-Milhim said. “They were Islamist, but not radical.”

But his view is not shared by all Arab Syrians.

Mann Aldaneh, a tribal leader of several Bedouin Arab villages near the Turkish border, has warm relations with nearby Kurdish villages.

He welcomed the agreement but said he did not trust the new central government in Damascus to guard prisons and camps in the northeast that hold thousands of Islamic State fighters and some 40,000 of their family members.

That sentiment has been echoed by security officials in neighboring Iraq and Europe as well.